Contacts of the helix formed by residues 159 - 170 (chain J) in PDB entry 3A68
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 159 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40J LYS 3.3 12.1 - - - +
41J TYR* 3.4 14.2 - - - -
42J VAL 4.9 0.3 + - - -
45J SER* 4.1 15.4 + - - +
105J ARG* 3.0 44.1 + - - -
154J ALA* 2.8 20.5 + - - +
155J THR* 5.8 0.4 - - - -
157J ASN* 3.3 3.7 - - + +
158J GLY* 1.3 69.3 - - - +
160J VAL* 1.3 65.1 + - - +
161J GLN* 3.5 2.4 + - - +
162J LEU* 3.0 20.1 + - + +
163J ALA* 3.1 23.4 + - - +
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Residues in contact with VAL 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J GLY 3.2 11.8 + - - +
159J ASP* 1.3 73.7 + - - +
161J GLN* 1.3 58.8 + - - +
163J ALA* 3.4 6.3 + - - +
164J ASP* 3.0 25.8 + - - +
148Q LEU* 4.3 17.9 - - + +
151Q HIS* 3.3 46.4 - - + +
167Q GLU* 4.1 6.4 - - + +
171Q LEU* 3.5 20.9 - - + -
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Residues in contact with GLN 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J TYR* 2.5 36.3 + - - -
105J ARG* 3.9 9.6 + - - +
159J ASP* 3.4 2.5 + - - +
160J VAL* 1.3 78.3 - - - +
162J LEU* 1.3 62.8 + - - +
164J ASP* 3.3 9.1 + - + +
165J PHE* 2.8 39.4 + - - +
148Q LEU* 5.4 4.1 - - + +
167Q GLU 5.8 0.2 + - - -
171Q LEU* 3.7 36.1 - - + +
172Q GLY* 3.6 18.4 - - - +
175Q VAL* 3.7 22.5 - - + +
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Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J TYR* 4.5 2.9 - - + -
45J SER* 3.9 29.8 - - - +
49J VAL* 3.9 22.7 - - + -
98J LEU* 5.9 0.4 - - + -
101J TYR* 3.2 35.1 + - + +
105J ARG* 4.0 2.0 - - - +
150J LEU* 4.4 11.4 - - + -
153J VAL* 6.0 0.2 - - + -
154J ALA* 3.6 22.0 - - + +
159J ASP* 3.0 22.0 + - + +
161J GLN* 1.3 73.1 - - - +
163J ALA* 1.3 67.6 + - - +
165J PHE* 3.3 3.3 + - + -
166J VAL* 3.0 44.9 + - + +
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Residues in contact with ALA 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J HIS* 3.5 24.7 - - + +
154J ALA* 3.8 15.0 - - + +
155J THR* 4.3 10.5 - - - +
159J ASP 3.1 18.6 + - - +
160J VAL* 3.7 6.3 - - - +
162J LEU* 1.3 76.8 - - - +
164J ASP* 1.3 58.1 + - - +
166J VAL* 3.4 1.0 + - - -
167J GLU* 3.0 37.1 + - - +
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Residues in contact with ASP 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160J VAL 3.0 16.8 + - - +
161J GLN* 3.7 13.3 + - + +
162J LEU 3.2 0.2 - - - -
163J ALA* 1.3 75.8 - - - +
165J PHE* 1.3 58.9 + - - +
167J GLU* 3.4 11.4 + - - +
168J THR* 2.8 47.2 + - - -
167Q GLU* 3.2 40.4 - - + +
168Q THR* 4.6 3.6 + - - -
171Q LEU* 6.0 0.4 - - + -
363Q CA 2.6 27.5 - - - -
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Residues in contact with PHE 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J LYS* 4.1 18.2 - - + -
98J LEU* 3.8 15.9 - - + -
101J TYR* 3.6 59.5 - + + -
104J LYS* 6.0 3.8 - - - -
161J GLN* 2.8 28.9 + - - +
162J LEU* 3.6 6.1 - - + +
164J ASP* 1.3 72.8 + - - +
166J VAL* 1.3 67.1 + - + +
168J THR* 4.7 3.4 - - - -
169J GLU* 2.9 56.4 + - + +
170J TYR* 3.7 28.5 - + - -
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Residues in contact with VAL 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J LEU* 3.9 33.0 - - + +
150J LEU* 3.7 27.8 - - + -
151J HIS* 4.2 13.5 - - + +
162J LEU* 3.0 30.4 + - + +
163J ALA* 3.7 5.4 - - - +
165J PHE* 1.3 82.9 - - + +
167J GLU* 1.3 62.7 + - - +
170J TYR* 3.0 25.3 + - + +
171J LEU* 3.2 25.0 + - + -
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Residues in contact with GLU 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J HIS* 2.6 34.2 + - + +
163J ALA* 3.0 26.3 + - - +
164J ASP* 3.6 14.6 - - - +
166J VAL* 1.3 78.1 - - - +
168J THR* 1.3 63.7 + - - +
171J LEU* 3.4 25.1 + - + +
172J GLY 3.9 4.2 + - - -
160N VAL* 3.9 15.2 - - + +
164N ASP* 3.3 40.4 - - - +
361N CA 4.1 8.1 - - - -
167Q GLU* 5.7 0.3 - - - +
363Q CA 4.0 3.5 - - - -
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Residues in contact with THR 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J ASP* 2.8 40.4 + - - -
165J PHE* 4.1 2.7 - - - -
167J GLU* 1.3 74.8 - - - +
169J GLU* 1.3 77.7 + - - +
173J GLU* 3.6 1.0 - - - +
215J CA 2.4 28.7 - - - -
164N ASP* 4.6 7.2 + - - -
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Residues in contact with GLU 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J LYS* 2.9 38.4 + - - +
165J PHE* 2.9 45.9 + - + +
168J THR* 1.3 93.1 - - - +
170J TYR* 1.3 76.7 + - + +
173J GLU* 3.3 23.3 - - - +
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Residues in contact with TYR 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J GLU* 4.3 6.1 - - - -
94J HIS* 2.7 52.6 + + + -
97J LYS* 3.3 22.7 - - - +
98J LEU* 3.2 24.4 - - + +
147J LEU* 3.8 35.1 - - + +
150J LEU* 6.5 0.2 - - + -
165J PHE* 3.7 33.0 - + - -
166J VAL* 3.0 20.4 + - + +
168J THR 3.5 0.6 - - - -
169J GLU* 1.3 93.6 - - + +
171J LEU* 1.3 57.9 + - - +
172J GLY 3.5 2.2 - - - -
173J GLU* 3.4 4.8 + - - +
174J GLN* 2.9 32.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il